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Yorodumi- PDB-6pfe: Crystal structure of TS-DHFR from Cryptosporidium hominis in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6pfe | |||||||||
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Title | Crystal structure of TS-DHFR from Cryptosporidium hominis in complex with NADPH, FdUMP and 2-(4-((2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl)benzamido)-4-methoxybenzoic acid. | |||||||||
Components | Bifunctional dihydrofolate reductase-thymidylate synthase | |||||||||
Keywords | transferase/transferase inhibitor / Inhibitor / TS / TS-DHFR / TRANSFERASE / transferase-transferase inhibitor complex | |||||||||
Function / homology | Function and homology information thymidylate synthase activity / dTMP biosynthetic process / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / methylation Similarity search - Function | |||||||||
Biological species | Cryptosporidium hominis (eukaryote) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.812 Å | |||||||||
Authors | Czyzyk, D.J. / Valhondo, M. / Jorgensen, W.L. / Anderson, K.S. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Eur.J.Med.Chem. / Year: 2019 Title: Structure activity relationship towards design of cryptosporidium specific thymidylate synthase inhibitors. Authors: Czyzyk, D.J. / Valhondo, M. / Deiana, L. / Tirado-Rives, J. / Jorgensen, W.L. / Anderson, K.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6pfe.cif.gz | 519.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pfe.ent.gz | 427.7 KB | Display | PDB format |
PDBx/mmJSON format | 6pfe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pf/6pfe ftp://data.pdbj.org/pub/pdb/validation_reports/pf/6pfe | HTTPS FTP |
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-Related structure data
Related structure data | 6pf3C 6pf4C 6pf5C 6pf6C 6pf7C 6pf8C 6pf9C 6pfaC 6pfbC 6pfcC 6pfdC 6pffC 6pfgC 6pfhC 6pfiC 4q0eS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
-Protein , 1 types, 5 molecules ABCDE
#1: Protein | Mass: 60262.520 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cryptosporidium hominis (eukaryote) / Gene: CHUDEA4_4460 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): PA-414 / References: UniProt: A0A0S4TER9 |
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-Non-polymers , 5 types, 60 molecules
#2: Chemical | ChemComp-NDP / #3: Chemical | ChemComp-UFP / #4: Chemical | ChemComp-OEA / #5: Chemical | ChemComp-MTX / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.6 Å3/Da / Density % sol: 73.3 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Well Solution 18 % PEG 6000, 0.2 M ammonium sulfate, 0.06 M lithium sulfate, 0.1 M Tris Drop Ratio 2:1 enzyme mix/well solution |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 15, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 124669 / % possible obs: 95.5 % / Redundancy: 6 % / CC1/2: 0.984 / Rsym value: 0.254 / Net I/σ(I): 5.78 |
Reflection shell | Resolution: 2.8→2.97 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 0.83 / Num. unique obs: 17614 / CC1/2: 0.5 / Rsym value: 1.629 / % possible all: 84.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4Q0E Resolution: 2.812→49.438 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.55
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.812→49.438 Å
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Refine LS restraints |
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LS refinement shell |
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